In the eastern part of Lake Constance, the second largest pre-alpine Lake in Europe, about five hundred pockmarks (morphological depressions on the lake floor) were recently discovered of which ~ 40% release methane bubbles. The carbon isotopic composition of the escaping gas indicated that the methane is of biogenic origin. In our study, we investigated the fate of the released methane bubbles, i.e., the dissolution, oxidation or transport of the bubbles to the surface. At a littoral pockmark site (PM12, 12 m water depth) and a profundal pockmark (PM80, 80 m water depth), we analysed the dissolved methane concentrations and the methane isotopic carbon signature in the water column. At PM80, higher methane concentrations (up to 1523 nM), compared to the control site and the surface waters (225 ± 72 nM), were recorded only on some occasions and only in the bottom water, despite the fact that the released bubbles were dissolving within the hypolimnion based on bubble modeling. The isotope data suggest that most of the dissolved methane is oxidized below 40 m water depth. The isotopic signature of the methane in the surface water at PM80, however, differed from that of the methane in the hypolimnion; therefore, the surface methane at this profundal site is most likely an export product from the littoral zone. Assuming an initial bubble diameter of 5 mm, we calculated that these small bubbles would reach the surface, but approximately 96% of the methane would have dissolved from the bubble into the hypolimnion. At PM12, we observed higher concentrations of dissolved methane (312 ± 52 nM) with no significant differences between seasons or between control sites versus pockmark site. In the shallow water, divers estimated the bubble size to be 10 - 15 mm, which from a release depth of 12 m would barely dissolved in to the water column. The isotopic signature also indicated that there had been almost no methane oxidation in the shallow water column. Thus, the water depth of bubble release as well as the initial bubble size determine whether the methane enters the atmosphere largely unhindered (shallow site) or if the released methane is incorporated into the profundal water column.